Michael W. Ackerman

Single-Nucleotide Polymorphisms (SNPs) under Diversifying Selection Provide Increased Accuracy and Precision in Mixed-Stock Analyses of Sockeye Salmon from the Copper River, Alaska

Abstract Genetic markers are increasingly being used to ascertain the population of origin of individuals or mixtures of individuals in complex aggregations of Pacific salmon Oncorhynchus spp. Multilocus genotype data from single-nucleotide polymorphisms (SNPs) are especially useful for admixture analyses. Single-nucleotide polymorphisms can be discovered in nonmodel organisms with relative ease and can be characterized in the coding and regulatory regions of the genome influenced by selection. Those influenced by diversifying selection may show atypically high levels of differentiation among populations and thus be particularly valuable for genetic stock identification in cases where neutral loci show little difference among populations of interest. We identified four SNP loci from a panel of 42 as candidates for diversifying selection (referred to here as nonneutral SNPs) in sockeye salmon O. nerka from the Copper River and adjacent coastal drainages in south-central Alaska. We evaluated the information...

Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non‐neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non‐neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad‐scale population structure consistent with previous studies, but fine‐scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non‐neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non‐neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long‐term conservation of this species.

Estimating Abundance and Life History Characteristics of Threatened Wild Snake River Steelhead Stocks by Using Genetic Stock Identification

Abstract Assessments of threatened wild Snake River steelhead Oncorhynchus mykiss have historically been limited due to a lack of stock-specific information and difficulties in field sampling efforts. We used genetic stock identification (GSI) to estimate the composition of wild adult steelhead migrating past Lower Granite Dam on the Snake River between August 24 and November 25, 2008. Further, we combined genetic data with information on sex, length, age, and run timing to examine for differences in life history or demography among stocks. In total, 1,087 samples collected at the dam were genotyped with 13 standardized steelhead microsatellite loci and a new modified Y-chromosome-specific assay that differentiates sex. A genetic baseline of 66 populations was used to complete GSI of unknown-origin samples from Lower Granite Dam. Large differences in reporting group (stock) contributions were observed for the run as a whole; the Snake River–lower Clearwater River reporting group had the largest single con...

Effective number of breeders from sibship reconstruction: empirical evaluations using hatchery steelhead

Effective population size (Ne) is among the most important metrics in evolutionary biology. In natural populations, it is often difficult to collect adequate demographic data to calculate Ne directly. Consequently, genetic methods to estimate Ne have been developed. Two Ne estimators based on sibship reconstruction using multilocus genotype data have been developed in recent years: sibship assignment and parentage analysis without parents. In this study, we evaluated the accuracy of sibship reconstruction using a large empirical dataset from five hatchery steelhead populations with known pedigrees and using 95 single nucleotide polymorphism (SNP) markers. We challenged the software COLONY with 2,599,961 known relationships and demonstrated that reconstruction of full‐sib and unrelated pairs was greater than 95% and 99% accurate, respectively. However, reconstruction of half‐sib pairs was poor (<5% accurate). Despite poor half‐sib reconstruction, both estimators provided accurate estimates of the effective number of breeders (Nb) when sample sizes were near or greater than the true Nb and when assuming a monogamous mating system. We further demonstrated that both methods provide roughly equivalent estimates of Nb. Our results indicate that sibship reconstruction and current SNP panels provide promise for estimating Nb in steelhead populations in the region.

Maximum Likelihood Estimation of the Proportion of Hatchery-Origin Fish on Spawning Grounds Using Coded Wire Tagging and Parentage-Based Tagging

AbstractFor salmon populations in the Columbia River and Snake River basins, many of which are listed under the U.S. Endangered Species Act of 1973, reliable estimates of the proportion of hatchery-origin adults in spawning areas (p) are needed to assess population status and the genetic and demographic interactions of hatchery- and natural-origin fish. Some hatchery fish receive visible marks, coded wire tags (CWTs), parentage-based tags (PBTs), or all three. This allows one to identify whether fish recovered after release are of hatchery origin. Parentage-based tagging involves genotyping hatchery broodstock and uses parentage assignments as “tags” that identify the origin and brood year of their progeny. We derived a maximum likelihood estimator of p and applied it to the 2012 and 2013 carcass survey data for spring–summer Chinook Salmon Oncorhynchus tshawytscha in the South Fork Salmon River, Idaho. Maximum likelihood estimation was also applied to CWT data and, for investigating the importance of exp...

Life History Diversity of Snake River Steelhead Populations between and within Management Categories

AbstractGrouping populations for management may overlook the fine-scale diversity underpinning the stability and resilience of meta-populations and fisheries. A bimodal timing distribution of summer-run steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) historically was observed at Bonneville Dam (BON), the first barrier to upstream migration in the Columbia River basin. Early mode fish (A-run) tended to be younger and smaller (<78 cm) than later fish (B-run). While A-run fish spawn throughout the Columbia River basin, B-run fish spawn primarily in the Snake River basin. Managers used indices of these modes to make fishery decisions, and later these criteria were adopted for conservation. It is still unclear how life history and body size differences among wild Snake River populations are related to the categories at BON. We examined population parameters characterizing the two categories (date of passage at BON, length) and parameters directly affecting population dynamics (age composition, sex rat...